Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture

ES cells were differentiated as embryoid bodies in 10% FBS or serum-free media containing BMP4 (2 ng/ml), and expression profiled using 47 K Illumina(R) Sentrix arrays. Statistical methods were employed to define gene sets characteristic of stem cell, epiblast and primitive streak programs. Although the initial differentiation profile was similar between the two culture conditions, cardiac gene expression was inhibited in serum whereas blood gene expression was enhanced. Also, expression of many members of the Kruppel-like factor (KLF) family of transcription factors changed dramatically during the first few days of differentiation. KLF2 and KLF4 co-localized with OCT4 in a sub-nuclear compartment of ES cells, dynamic changes in KLF-DNA binding activities occurred upon differentiation, and strong bio-informatic evidence for direct regulation of many stem cell genes by KLFs was found.Down regulation of stem cell genes and activation of epiblast/primitive streak genes is similar in serum and defined media, but subsequent mesoderm differentiation is strongly influenced by the composition of the media. In addition, KLF family members are likely to be important regulators of many stem cell genes.Embryonic stem (ES) cells isolated from the inner cell mass of the early mammalian blastocyst-stage embryo retain pluripotency when cultured on mouse embryonic fibroblasts (MEFs) in the presence of leukemia inhibitory factor (LIF) [1]. In the absence of LIF and MEF attachment, ES cells spontaneously differentiate into multi-cellular aggregates termed embryoid bodies (EBs). Although the spatial complexity of organogenesis is not established during EB maturation, the dynamics of gene expression closely mimic those which characterize early stages of mouse development [2-5]. Thus, ES cell differentiation is an excellent model system for the discovery of genes involved in developmental processes.Many studies have attempted to identify genes that define the stem cell state by mining fo